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Univerzita Karlova V Praze Přírodovědecká Fakulta Univerzita Karlova v Praze Přírodovědecká fakulta Studijní program: biologie Studijní obor: zoologie Dmytro Omelchenko Genetická variabilita rodu Alburnoides v Ázerbajdžánu Genetic variability of the genus Alburnoides in Azerbaijan Diplomová práce Školitel: RNDr. Miroslav Švátora, CSc. Konzultant Mgr. Radek Šanda, PhD. Praha, 2016 Prohlášení: Prohlašuji, že jsem práci vypracoval samostatně s použitím uvedené literatury. Práce je psána v jazyce anglickém a nebyla v ní provedena jazyková korektura. Anglický jazyk byl zvolen pro usnadnění vzniku budoucí odborné publikace a možnost případné konzultace se zahraničními odborníky. Tato práce ani její podstatná část nebyla předložena k získání jiného nebo stejného akademického titulu. V Praze, 15. 08. 2016 ................................................. Dmytro Omelchenko Acknowledgements Rád bych poděkoval mým rodičům za veškerou podporu během studia biologie. Děkuji svému školiteli Miroslavu Švátorovi za navržené téma, konzultace a průvod akademickým prostředím Univerzity Karlovy. Chtěl bych také poděkovat svému konzultantovi Radkovi Šandovi za cenné rady a připomínky, finanční podporu a též za vedení v průběhu praktické části této studie. Taktéž děkuji Zuzaně Musilové za pomoc se sestavováním teto práce a přípravu fylogenetických analýz a v neposlední řadě za přátelský přístup. Dále děkuji Akifu Gulievu a kolektivu státní univerzity v Baku za pomoc v organizaci terénní práce a sběru materiálu. Chci poděkovat Danielu Fryntovi za konstruktivní připomínky k interpretaci výsledků. Rad bych poděkoval Zuzaně Varadinové a Dovile Barčytě za pomoc a školení v laboratoři. Také děkuji Zdeňku Lerchovi, Milanu Kaftanovi, Evě Landové a Barbarě Kaftanové za spoluúčast při expedici do Ázerbajdžánu. Abstract: The Caucasus region is characterized by high rate of endemism and taxa richness of fishes. Azerbaijan is a country situated on the border between Europe and Asia with rivers flowing in the Caspian Sea. Natural environment of this country is represented by various habitats with diverse ichthyofauna. This region is very attractive for biogeographical studies because it lays on the border of two different ecoregions. Even on the modern stage of scientific cognition, there is still lack of data about freshwater fishes from that region. Spirlins or rifle-minnows (Alburnoides Jeitteles, 1861, Actinopterygii, Cyprinidae) is a genus of small freshwater fishes and it has been chosen as a focus of this thesis because of numerous reports of new species from surrounding countries. The presented thesis is one of the seldom molecular studies trying to reveal the taxonomical situation within the genus Alburnoides, describe the phylogenetic relationships between geographically isolated populations, and provide biogeographical implications for fishes in the Caspian Sea river basins. Both mitochondrial (cytochrome b, cytochrome oxidase subunit I) and nuclear (RAG1, rhodopsin) markers were used in the study and the Maximum Likelihood, Maximum Parsimony and Bayesian phylogenetic analyses were performed. Further, the method of Molecular Clock was applied to estimate divergence between linages inside genus Alburnoides and for subsequent constructing of biogeographical scenario. High level of genetic variability has been found within the genus Alburnoides in Azerbaijan. Examined individuals represent three well- supported major clades in phylogenetic trees, some of them (but not all) corresponding to the geographically isolated localities. The population structure and haplotype distribution within the Alburnoides genus cannot be explained only by geographical isolation. There is a putatively undescribed species, Alburnoides sp. 5 in Ciscaucasian region, a lineage which probably diverged as a result of a vicariant event. Identified lineage richness within the samples from the Talysh Mountains hydrological network probably show the evidence for the existence of glacial refugium in the region. The regions in the North (Greater Caucasus hydrological network) were genetically uniform, while the localities in the South (Talysh Mountains hydrological network) were composed of two different lineages. This brings an evidence for putative colonization events from the North to the South, which might have been facilitated by the known currents in the Caspian Sea. Newly reported invasive species for the Azerbaijan ichtyofauna, Hemiculter leucisculus, has been registered. Keywords: Alburnoides, biogeography, fish, genetic variability, phylogeny. Abstrakt: Region Kavkazu je charakterizován vysokou úrovní endemizmu a bohatstvím taxonů ryb. Ázerbájdžán je stát, který je situovaný na rozhrání mezi Evropou a Asii, a jeho řeky tečou do Kaspického moře. Přírodní prostředí tohoto státu představují různorodé habitaty s diversifikovanou faunou a daný region je velmi atraktivní také pro biogeografický výzkum, jelikož leží na rozhraní dvou různých ekoregionů. I v současné době stále chybějí podrobné znalosti o sladkovodních rybách z toho regionu. Ouklejky (Alburnoides Jeitteles, 1861, Actinopterygii, Cyprinidae) jsou rodem drobných sladkovodních ryb, které byly vybrány jako objekt výzkumu také kvůli početným objevům a popisům nových druhů z okolních států. Předkládaná práce je jedná z mála molekulárních studií, která se pokouší vyřešit taxonomickou situaci uvnitř rodu Alburnoides, popsat fylogenetické vztahy mezi jednotlivými populacemi a poskytnout biogeografické interpretace pro ichtyofaunu z povodí řek Kaspického moře. V práci byly použity jak mitochondriální (cytochrom b, cytochrom oxidáza podjednotka I) tak i jaderné (RAG1, rodopsin) markery a analýzy maximální věrohodnosti (Maximum Likelihood), maximální parsimonie (Maximum Parsimony) a Bayesovské analýzy byly použité k rekonstrukci fylogenetických a fylogeografických vztahů. Dále byla použita metoda molekulárních hodin (Molecular Clock) pro odhad času divergence mezi jednotlivými liniemi uvnitř rodu Alburnoides a pro následnou rekonstrukci biogeografického scénáře. Byla potvrzena výrazná genetická variabilita uvnitř rodu Alburnoides v Ázerbájdžánu. Zkoumaní jedinci ve fylogenetických stromech tvoří tři dobře podpořené linie (clades); někteří z těchto linií jsou vázány výlučně na geograficky vzdálené a izolované lokality. Populační struktura a distribuce haplotypů nemůže být ovšem vysvětlena jen na základě geografické izolace. Rodová linie nepopsaného druhu Alburnoides sp. 5 z Předkavkazska se hypoteticky oddělila následkem vikariantní události. Zjištěné bohatství rodových linií mezi vzorky z hydrologické sítě Talyšských Hor je pravděpodobně důkazem existence glaciálního refugia v regionu. Populace na severu Ázerbajdžánu (hydrologická síť Velkého Kavkazu) jsou geneticky uniformní, zatímco lokality na jihu (hydrologická síť Talyšských hor) byly obývány dvěma nezávislými liniemi ouklejek, což by mohlo být následkem kolonizačních událostí směrem ze severu na jih, které mohly být také usnadněny díky proudům v Kaspickém moři. Invazivní druh Hemiculter leucisculus nedávno popsaný pro faunua Ázerbajdžánu byl zaregistrován také během terénních sběrů použitých pro tuto práci. Klíčová slova: Alburnoides, biogeografie, fylogeneze, genetická variabilita, ryby. Contains: 1 Introduction ........................................................................................................... 8 2 Literature overview ............................................................................................... 9 2.1 Overview of the genus Alburnoides. Insights into morphology, taxonomy and evolution. ................................................................................................................................. 9 2.2 Biogeography of Alburnoides genus ................................................................ 11 2.3 Fossil record of Cyprinid fishes ....................................................................... 13 2.4 Biogeographical delineation of the research region ........................................ 14 2.5 Geological history of Caucasus and Caspian Sea ............................................ 19 3 Main goals of present study ................................................................................ 25 4 Materials and methods ........................................................................................ 26 4.1 Samples collection ........................................................................................... 26 4.2 DNA extraction and PCR ................................................................................ 27 4.3 Dataset preparation .......................................................................................... 28 4.3.3 Datasets for MP, ML and Bayesian methods. .............................................. 28 4.3.2 Haplotype network dataset ............................................................................ 29 4.3.3 Concatenation of genes ................................................................................. 29 4.4 Model testing ................................................................................................... 29 4.5 Maximum likelihood method ........................................................................... 30 4.6 Maximum Parsimony ....................................................................................... 30 4.7 Bayesian analysis ............................................................................................. 30 4.8 Haplotype network ........................................................................................... 31
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